NCSU Biochemistry graduates stellar students

May Graduation 2013

May Graduation 2013

In the May 2013 graduation ceremony, the department conferred BS Biochemistry degrees to 56 students and PhD Biochemistry to 5 students.

Previous graduating classes were approximately 40:60 men:women; the current class is just about even at 52:48 [same as the ratio for December 2012 graduation!]. There was good diversity of the students who specified their ethnicity: 43% – non Caucasian with 20% Asian, 2% Hispanic, 11% Afro-American, 4% American Indian and 5% mixed.

The undergraduate students were quite accomplished, with an average GPA of 3.35.

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New Course Offered: ‘Physical Chemistry for Life Scientists’

Chuck Hardin

Chuck Hardin

Have you seen the bumper sticker “Honk if you passed P-Chem”? I recently finished teaching the first semester of a new course offering designed to make P-Chem “come alive” for our students.

It seems obvious to me that every dry, hyper-theoretical lesson one encounters in the standard P-Chem course deserves to be refocused to highlight how it bears on biochemistry. Not only does it reveal how the biochemistry works, it also provides a much more interesting and example-driven way to actually hook into the concepts. For example, we learned about diffusion theory by covering the limitations placed on the use of pheromones by the size of an organism and the rates of diffusion of both the pheromone and the organism. In another, we used the Boltzmann distribution to understand how voltage-gated ion-channels work. In a third, we looked at the use of lattice models and the canonical ensemble to understand how the search process that leads to protein folding works.

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Hardin and Knopp Publish New Textbook: ‘Biochemistry – Essential Concepts’

Chuck Hardin

Chuck Hardin

Editor’s Note: Drs. Chuck Hardin and Jim Knopp recently published a new textbook/workbook with Oxford University Press (2012, ISBN 97 80199 765621, website: OUP.com). Chuck described the process of publishing a book to Biochem Blogs.

So we wanted to publish a book? We had no idea what we were getting into. It turned out that developing, contracting and completing a textbook required way more than just writing the words. When viewed in the rearview mirror, it was more like pursuing and completing a research project.

Oxford really puts their authors through the ringer. For example, the book is full of illustrations. In fact, completing the composition process involved extracting 843 figures from the manuscript, documenting them, then sending them to the composition editor, who inserted all 843 figures into the officially composed print version. Whew!

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The traveling biochemist: Biochemistry in Dar es Salaam

Trino Ascencio-Ibanez

Trino Ascencio-Ibanez

Part 1: The multinational project

It sounds exotic, and it certainly is. Dar es Salaam is the biggest city in Tanzania, but is not the capital (Dodoma). It is a port with 2.5 million people in 2002 (last official census) and is also the richest city in the country. This is my second visit since I spent two weeks here in May 2012 training people in the use of the low pressure DNA acceleration device, qPCR for gene expression, cloning and Agrobacterium transformation. This time the purpose of my visit was quite different. In our research, Dr. Linda Hanley-Bowdoin and I have been collaborating with Dr. Joseph Ndunguru, director of the Mikocheni Agricultural Research Institute (MARI) in Dar es Salaam. He just received a Phase II grant from the Bill and Melinda Gates Foundation (BMGF) for 9.4 million US$. It is an international, multinational effort including sub-grantees from Tanzania, Kenya, Uganda, Rwanda, Malawi, Mozambique, Zambia, Rutgers University and North Carolina State University (Go Pack !!).

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Visiting Poznan as a Fulbright Senior Specialist Fellow

Hanna Gracz

Hanna GraczI'm on ScienceSeeker-Microscope

The Institute of Bioorganic Chemistry Polish Academy of Sciences (IBCH PAS) was established almost 25 years ago, but its origins date back to 1969 when the Department of Stereochemistry of Natural Products was brought into being at the Institute of Organic Chemistry PAS. In 1980, the Department of Stereochemistry of Natural Products was transformed into an independent entity – Department of Bioorganic Chemistry PAS. In 1988, the latter was finally converted into the Institute of Bioorganic Chemistry Polish Academy of Sciences. Today, together with the affiliated Poznan Supercomputing and Networking Center, the IBCH PAS has more than 460 staff members, including 80 research scientists (33 Professors). In addition, about 80 Ph.D. students are currently involved in the research projects conducted at IBCH PAS.

gracz1gracz2The scientific portfolio of the Institute has many dimensions: synthesis and structure of natural products, in particular nucleic acids and their components; biochemistry, molecular and structural biology of model biological systems, genetic engineering, genomics and bioinformatics. IBCH PAS is authorized to confer the degree of doctor and habilitated doctor in chemistry and biochemistry.

The Institute is organized into 12 research departments and 10 research groups. Within the structure of the Institute, there are also other crucial units associated: the PAS Poznan Science Center, Scientific Publishers, Guest Rooms ( I like this place), and Library. In the latest years, the Institute in collaboration with the Poznan University of Technology have created a European Center for Bioinformatics and Genomics, a unique unit in Poland.

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Listening sessions for strategic planning

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

As some of you may know, NC State University is undergoing one of the largest restructuring endeavors in the history of the university. Several academic departments currently in the College of Agriculture and Life Sciences (CALS) are moving to the new College of Sciences (COS). Other departments in COS will include those already in the college of Physical and Mathematical Sciences (PAMS).

Left in CALS will be our department, Molecular and Structural Biochemistry, and Plant Biology – the two remaining departments from the “Life Sciences” side of CALS – and several faculty from other departments who will not be moving to COS along with their department.

As part of the restructuring at NCSU, CALS is undertaking a strategic planning process and will produce an action plan by June of this year. The plan will then be implemented starting next academic year, July 2013.

In order to gather input for the strategic planning process, Dean Rich Linton and his team will hold several “listening sessions” around the state of North Carolina in order to get input from college stakeholders. The first sessions begin next week, on Monday January 7, 2013.

We need your help.

While traditional agriculture departments have clear “stakeholders” in their state commodity groups, the stakeholders for Life Science departments are less clear. How do we in Life Sciences define our stakeholders when our primary research projects focus on fundamental (basic) mechanisms of plant and/or animal growth and development? Unlike the traditional agricultural departments, Life Science departments do not utilize lobby groups or contain boards organized around specific applied research outcomes.

So, who are our stakeholders? Undergraduate and graduate students? Alumni? Current and former faculty? Staff? Research scientists in North Carolina and throughout the world? CEOs and other officers of biomedical, biotechnology, or agribusiness companies? Funding agencies?

Yes. All of the above. But, funding agencies are unlikely to provide input into the strategic planning process, so we need your input. If you are a student, former student, post-doctoral associate, research scientist, science teacher, CEO, CSO, member of the staff, or simply someone who has an interest in the future of the college, then please visit the strategic planning website at the link below, and give us your opinion.

 A New Chapter: CALS Strategic Plan 2013

The website provides a timeline for events in strategic planning and a link to the survey (**Take Our Stakeholder Survey**). The few minutes you spend will be invaluable to shaping the vision of Life Sciences in CALS. In particular, your input will help to shape the future of the Biochemistry Department in the newly restructured college. Using the information you and others provide, several working groups will construct the blueprints for restructuring CALS.

If you live in North Carolina and can attend any of the listening sessions, then we would welcome your comments in person. A list of dates and registration information can be found on the same site.

An invitation from the Dean, with specific insight requested, is reproduced below.

December 20, 2012
CALS Faculty, Staff, Students, and other Stakeholders: As you probably have heard by now, on December 11, 2012 the College of Agriculture and Life Sciences (CALS) embarked on a new college strategic planning process. The steering committee and Department Heads have been involved in early planning sessions with our strategic planning consulting firm, Tecker International, LLC. This is an exciting time in the CALS as this process will provide many opportunities for engagement and involvement by faculty, students, staff, stakeholders, alumni, donors and other supporters in charting the future direction we take as we tackle the significant societal challenges facing our state, nation and world.

Later today, an announcement and invitation to participate in this process will be sent via multiple email lists. We encourage you to carefully review the information you will receive and find ways to interact with this process via listening sessions, working groups and other opportunities that will be provided in the coming weeks. You will see that we will be conducting listening sessions on campus and across the state to solicit input and ideas. We hope that you will take advantage of this opportunity to be involved in the process. After the listening sessions are conducted, working groups will be established to focus on specific issues and challenges related to the future of the College.

This is a critically important process for the College as we have the opportunity to develop a strategic plan and also an on-going process for strategic visioning that will allow us to have greater impact in our state, nation and world.

Thanks for all that you are doing to make the College and University extraordinary. We look forward to working with you as the process unfolds in the coming months.
Richard Linton
Dean of CALS

Top Biochem Blogs of 2012

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

In the first year of the Biochem Blogs we posted sixty-two blogs on a variety of topics, including cancer biology, intrinsically disordered proteins, circular proteins, bioanalytical techniques, reports from conferences, international travel, advice to young scientists, sh*t graduate students say – even a discussion from the One Word Professor on evolution theory. The top five blogs of the year, based on total number of views, include humor, videos, and some serious science.

In reverse order, the top Biochem Blogs of 2012 are:

 

Zebrafish modified to grow tumors

Zebrafish modified to grow tumors

5. Using zebrafish to find human cancer drugs (posted April 2, 2012). We submitted a proposal for an internal grant at NC State, and the grant had to be in the form of a video. The winner was chosen based on total votes from a website as well as votes collected the day of the conference. Our submission didn’t win, but we had a great time making the video.

Profiling techniques

miRNA profiling techniques

4. Finding biomarkers for human cancer: miRNA profiling (posted May 1, 2012). Graduate student Chunxiao Ma describes recent research on how the newly discovered miRNA shows an advantage in distinguishing cancer types. miRNAs are a group of short non-coding RNAs that negatively regulate gene expression at the post-translational and/or translational level. The innate advantage of using an miRNA profile is that there are only about 200 miRNA discovered in the cell. A number of research articles show that a specific miRNA or a cluster of miRNA influences each stage of cancer development. Based on recent research, miRNA expression profiles could serve as a classifier of human cancers.

stressed scientist

Stressed scientist

3. Timeline for stress-free grant writing (posted April 26, 2012). Writing a grant can be a stressful time for a scientist. How can one write a competitive grant with great prose, great preliminary results, and cutting-edge ideas? We can’t help with that, but we can help you hit specific milestones in grant writing so that you can lower your stress level and ensure that you get the grant submitted by the deadline. Remember – the only certainty in science is that if you don’t write the grant, it’s guaranteed not to get funded. So, follow our timeline for writing your grant and lower your stress. {Disclaimer: Biochem Blogs is not responsible for low funding rates or the high probability that you will revise/resubmit your proposal.}

Norbornene labeled protein rapidly reacts with tetrazine compounds

Norbornene labeled protein rapidly reacts with tetrazine compounds, from Lang et al., DOI 10.1038/NCHEM.1250

2. A genetically encoded site-specific label for protein imaging (posted March 7, 2012). In recent years, several chemical probes have been developed that allow the incorporation of reactive tags into proteins. The tags can then be modified within the complex mixture of the cellular milieu, providing a powerful technique to examine protein structure and function as well as interaction networks in native conditions. In this blog, we describe the use of a bioorthogonal approach coupled to rapid reaction chemistry to label proteins. An advantage of the norbornene probe is that the protein can be labelled rapidly and selectively with tetrazine-based probes and monitored by fluorescence emission. The tetrazine-based probes have low background because they are “turn-on” fluorescent probes; the fluorescence is high only after reaction with the norbornene label on the protein.

And the top Biochem Blog of 2012 -

Favorite beers

Let’s have a beer

1. The graduate student path to beer (posted February 29, 2012). It had to be the beer, right? Because a good beer is worth the effort. Navigating the complexities of graduate school can be exhausting. One can work up a mighty thirst trying to fulfill the petty requirements of one’s graduate committee. Follow our advise on how to navigate the system. The reward is worth it because there’s always beer at the end of the path. Remember our formula for success: Success = 81.6% Perspiration + 10% Inspiration + 8.4% Alc. Oatmeal Stout

how to find beer

Success = 81.6% Perspiration + 10% Inspiration + 8.4% Alc. Oatmeal Stout

Confessions of a first time instructor

 

Dr. Greg Buhrman

Dr. Greg Buhrman

This is the second blog piece I’ve written, although it may be the first one you’ll read. Dr. Clay Clark asked me to blog about my experiences teaching BIO 414 (Cell Biology) for the first time. I wrote one piece half-way through the semester about one particularly interesting teaching experience. Then Clay asked me for the backstory but I never felt introspective enough to get into it. Now it’s the day before graduation and I’m feeling introspective, so here goes…

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A reflection on fifteen years of leadership

 

Clay Clark

Clay Clark - @biochemprof

Fifteen years ago Dr. Dennis Brown became the sixth head of the NC State Department of Biochemistry. He had served previously as the Director of the Cell Research Institute and Chair of the Division of Biological Sciences at UT Austin and came to NCSU with a mandate to build a strong structural biochemistry program. Prior to Dennis’ start at NCSU, the department had spent many years under the leadership of Dr. Paul Agris building a program in molecular biochemistry, particularly in the area of RNA structure and function.

The biochemistry department has thrived in the past 15 years, with a strong vision from the head as well as strong support from the administration. Dennis will step down as department head in June, and as I step into the headship on an interim basis, I want to take a moment to look back at some of the highlights of his tenure.

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